10 20 30 40 50 60 70 80 1MBO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER OXYGEN STORAGE 27-AUG-81 1MBO
TITLE STRUCTURE AND REFINEMENT OF OXYMYOGLOBIN AT 1.6 ANGSTROMS RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755
KEYWDS OXYGEN STORAGE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.E.V.PHILLIPS
REVDAT 9 05-MAR-14 1MBO 1 REMARK REVDAT 8 21-APR-10 1MBO 1 REMARK REVDAT 7 16-FEB-10 1MBO 1 LINK REVDAT 6 24-FEB-09 1MBO 1 VERSN REVDAT 5 01-APR-03 1MBO 1 JRNL REVDAT 4 30-SEP-83 1MBO 1 REVDAT REVDAT 3 19-APR-83 1MBO 1 REMARK REVDAT 2 07-MAR-83 1MBO 1 SEQRES REVDAT 1 03-FEB-82 1MBO 0
JRNL AUTH S.E.PHILLIPS JRNL TITL STRUCTURE AND REFINEMENT OF OXYMYOGLOBIN AT 1.6 A JRNL TITL 2 RESOLUTION. JRNL REF J.MOL.BIOL. V. 142 531 1980 JRNL REFN ISSN 0022-2836 JRNL PMID 7463482 JRNL DOI 10.1016/0022-2836(80)90262-4
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.E.V.PHILLIPS,B.P.SCHOENBORN REMARK 1 TITL NEUTRON DIFFRACTION REVEALS OXYGEN-HISTIDINE HYDROGEN BOND REMARK 1 TITL 2 IN OXYMYOGLOBIN REMARK 1 REF NATURE V. 292 81 1981 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.E.V.PHILLIPS REMARK 1 TITL STRUCTURE OF OXYMYOGLOBIN REMARK 1 REF NATURE V. 273 247 1978 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.E.V.PHILLIPS REMARK 1 TITL THE STRUCTURE OF OXY-MYOGLOBIN REMARK 1 REF ACTA CRYSTALLOGR.,SECT.A V. 34 55 1978 REMARK 1 REF 2 (SUPPLEMENT) REMARK 1 REFN ISSN 0567-7394
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CONSTRAINED RECIPROCAL-SPACE LEAST-SQUARES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1MBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 285 REMARK 285 THE ENTRY COORDINATES REMARK 285 ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. REMARK 285 REMARK 285 IN ORDER TO GENERATE THE CRYSTAL AU, APPLY THE REMARK 285 FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED REMARK 285 BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. REMARK 285 X0 1 -0.9627 0.0005 0.2706 55.0080 REMARK 285 X0 2 -0.0004 1.0000 -0.0033 0.0210 REMARK 285 X0 3 -0.2706 -0.0032 -0.9627 33.6530 REMARK 285 CRYSTAL AU = REMARK 285 (X0) * CHAINS A
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.52506 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA.
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 170 DISTANCE = 8.22 ANGSTROMS REMARK 525 HOH A 180 DISTANCE = 8.09 ANGSTROMS REMARK 525 HOH A 203 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 208 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 267 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 289 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 298 DISTANCE = 5.48 ANGSTROMS REMARK 525 HOH A 314 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 356 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 368 DISTANCE = 13.00 ANGSTROMS REMARK 525 HOH A 376 DISTANCE = 11.94 ANGSTROMS REMARK 525 HOH A 377 DISTANCE = 14.24 ANGSTROMS REMARK 525 HOH A 379 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A 380 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A 383 DISTANCE = 12.95 ANGSTROMS REMARK 525 HOH A 389 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH A 393 DISTANCE = 10.27 ANGSTROMS REMARK 525 HOH A 394 DISTANCE = 11.99 ANGSTROMS REMARK 525 HOH A 395 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 405 DISTANCE = 14.83 ANGSTROMS REMARK 525 HOH A 407 DISTANCE = 10.70 ANGSTROMS REMARK 525 HOH A 408 DISTANCE = 5.58 ANGSTROMS REMARK 525 HOH A 415 DISTANCE = 9.15 ANGSTROMS REMARK 525 HOH A 419 DISTANCE = 9.35 ANGSTROMS REMARK 525 HOH A 430 DISTANCE = 9.15 ANGSTROMS REMARK 525 HOH A 433 DISTANCE = 9.59 ANGSTROMS REMARK 525 HOH A 434 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH A 437 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 438 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH A 440 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH A 442 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A 444 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 8.23 ANGSTROMS REMARK 525 HOH A 457 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 470 DISTANCE = 7.25 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 155 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 155 NA 102.8 REMARK 620 3 HEM A 155 NB 91.4 89.0 REMARK 620 4 HEM A 155 NC 93.9 163.3 90.3 REMARK 620 5 HEM A 155 ND 93.8 88.1 174.5 91.1 REMARK 620 6 OXY A 555 O1 174.4 71.9 86.7 91.4 87.9 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 555
DBREF 1MBO A 1 153 UNP P02185 MYG_PHYCA 1 153
SEQRES 1 A 153 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 153 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 153 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY
HET SO4 A 154 5 HET HEM A 155 43 HET OXY A 555 2
HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE
HETSYN HEM HEME
FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 OXY O2 FORMUL 5 HOH *334(H2 O)
HELIX 1 A SER A 3 GLU A 18 1 16 HELIX 2 B ASP A 20 SER A 35 1 16 HELIX 3 C HIS A 36 LYS A 42 1 7 HELIX 4 D THR A 51 ALA A 57 1 7 HELIX 5 E SER A 58 LYS A 77 1 20 HELIX 6 F LEU A 86 THR A 95 1 10 HELIX 7 G PRO A 100 ARG A 118 1 19 HELIX 8 H GLY A 124 LEU A 149 1 26
LINK NE2 HIS A 93 FE HEM A 155 1555 1555 2.07 LINK FE HEM A 155 O1 OXY A 555 1555 1555 1.83
SITE 1 AC1 4 SER A 58 GLU A 59 ASP A 60 HOH A 227 SITE 1 AC2 22 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC2 22 HIS A 64 VAL A 68 LEU A 89 SER A 92 SITE 3 AC2 22 HIS A 93 HIS A 97 ILE A 99 TYR A 103 SITE 4 AC2 22 LEU A 104 HOH A 163 HOH A 217 HOH A 229 SITE 5 AC2 22 HOH A 234 HOH A 269 HOH A 337 HOH A 469 SITE 6 AC2 22 HOH A 472 OXY A 555 SITE 1 AC3 5 PHE A 43 HIS A 64 VAL A 68 HEM A 155 SITE 2 AC3 5 HOH A 341
CRYST1 64.530 31.050 34.930 90.00 105.79 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016104 0.000000 0.000000 0.00000
SCALE2 0.000000 0.032206 0.000000 0.00000
SCALE3 0.008096 0.000000 0.028629 0.00000